Jewish groups looking for signals from Egyptian President Mohamed Morsi regarding his views were appalled when one finally came -- in the form of a nod and what appeared to be a muttered “amen” to an imam’s call for God to “deal harshly” with the Jews.

Morsi's nod at Friday prayers Oct. 19 and a separate call from the Egyptian Muslim Brotherhood's top leader for Muslims to unite and use force against Israel in a "holy Jihad" have drawn expressions of alarm from Jewish groups.

The Anti-Defamation League released a statement expressing its "deepening concern over the anti-Semitic rhetoric coming from the highest echelons of Egyptian society." The Zionist Organization of America and the Simon Wiesenthal Center called on the Obama administration to cut off ties with the Muslim Brotherhood, the movement behind Morsi's Freedom and Justice Party, though the new Egyptian president formally resigned the party's head after his election.

The American Jewish Committee said it is reaching out to Egyptian officials for further clarification.

“AJC has a longstanding relationship with the Egyptian government, we are determined to maintain that relationship throughout his transition,” said Jason Isaacson, the AJC's international affairs director. “Whatever the views of Egyptian leaders, the fact remains Egypt is a neighbor of Israel, maintains a peace treaty with Israel and requires constant attention.”

Morsi, who assumed office in June, has done little since then to assuage concerns that his Muslim Brotherhood background would severely alter the most populous Arab nation’s relationship with the West and, more particularly, its peace with Israel.

“Anyone who thought the Muslim Brotherhood would moderate simply because it won elections doesn't understand how ideological the organization is, and doesn't understand how it is structured to resist moderation,” said Eric Trager, a fellow at the Washington Institute for Near East Policy.

Trager described a system in which it takes five to eight years to attain full membership in the Brotherhood, and during which aspirants are subject to tests that weed out moderates.

Jewish concerns about how Morsi will handle relations with Israel have mounted in recent weeks.

Addressing the United Nations General Assembly on Sept. 27, Morsi did not mention Israel by name once, although he spoke at length about the Palestinian cause. His only reference to Israel was as “a party in the international community” that denied Palestinian rights.

The text of Morsi's speech as prepared and distributed in advance by Egypt’s mission to the U.N. included a positive reference to the Arab League's 2002 peace initiative, which called for comprehensive peace and recognition of Israel in exchange for Israel’s withdrawal to the 1967 lines and a resolution to the Palestinian refugee issue in exchange. Yet Morsi, JTA has discovered, omitted that part in the speech he delivered.

Also removed in the remarks Morsi delivered was a vow that was included in the advance text to uphold international commitments -- an assurance that the United States has sought, particularly as it relates to the 1979 peace treaty with Israel.

Next, in October, in a public message, Mohammed Badie, the Muslim Brotherhood’s supreme guide, reportedly said that “Zionists only understand the language of force” and “increased their corruption throughout the world, shedding the blood of the people, trampling sanctuaries and holy places, desecrating even their own sanctuaries through their actions.”

Then, on Oct. 19, Morsi attended Friday services at a mosque in Mersa Matruh, an Egyptian seaport, at which the imam – a prominent local Brotherhood figure – prayed to God to “deal harshly with the Jews and those who are allied with them.” The Middle East Media Research Institute published video of the event in which Morsi appeared to nod and mouth “amen” to those words.

“The drumbeat of anti-Semitism in the 'new' Egypt is growing louder and reverberating further under President Morsi and we are increasingly concerned about the continuing expressions of hatred for Jews and Israel in Egyptian society and President Morsi's silence in the face of most of these public expressions of hate," the ADL said in a statement.

Morsi and the Brotherhood also have been consolidating their power. In August, Morsi replaced the leadership of the military -- long seen as a bulwark of support for maintaining strong ties wit the U.S. and upholding the peace treaty with Israel. He has also removed limits on the presidency that the junta that controlled Egypt after Hosni Mubarak’s ouster in early 2011 had inserted.

Joel Rubin, the director of government affairs for the Ploughshares Fund, said that much of this posturing has to do with internal political considerations as the Brotherhood seeks to consolidate its leading role in the Egyptian polity.

“He’s making a priority of maintaining the leadership profile,” said Rubin, who previously worked on Middle East issues as a congressional staffer and at the State Department. “He has a political base he speaks to.”

Trager said that the offending statements of the sort delivered by the imam were not uncommon in Egypt.

“What is as disturbing is that these prayers are ubiquitous in Egypt and a common feature,” Trager said. “It’s awful, the president sitting there and saying amen, but you have tens of millions of Egyptians saying amen.”

A poll in September commissioned by The Israel Project found 74 percent of Egyptians disapprove of the fact that Egypt maintains diplomatic relations with Israel. The poll, conducted by Greenberg Quinlan Rosner, was based on face-to-face interviews with 812 Egyptians and had a margin of error of 3.5 percent.

There are already disagreements between Congress and the Obama administration over how best to deal with the new Egyptian government. The State Department announced in September plans to maintain the $1.3 billion in military assistance to Egypt and to increase economic assistance and support for democratization programs.

Rep. Kay Granger (R-Texas), the chairwoman of the foreign operations subcommittee of the U.S. House of Representatives Appropriations Committee, immediately put a hold on $450 million in emergency aid, saying “I am not convinced of the urgent need for this assistance and I cannot support it at this time."

James Phillips, a senior fellow at The Heritage Foundation, said that giving the emergency aid “sends the wrong signals to the Egyptian government." He noted the two days it took for Morsi contain mob attacks on the U.S. embassy on Sept. 11 and publicly criticize them. “He has proven himself to be someone who can’t be counted on,” Phillips said.

But Rubin said the assistance, primarily designated for the military, helps bolster Egyptian moderates. Still, he said that it was appropriate for the Obama administration to make clear its unhappiness with anti-Semitic and anti-American pronouncements. He noted Obama’s declaration in an interview with Telemundo recently that Egypt was neither ally nor an enemy -- a significant downgrading of the status of Egypt, which has long been one of the leading recipients of U.S. aid.

“We should be comfortable in telling Morsi what we think is appropriate and telling him what we think the government of Egypt needs to be saying and not saying regarding Israel,” Rubin said.

Steven Cook, a senior fellow for Middle Eastern studies at the Council on Foreign Relations, said that the U.S. should closely watch areas where tensions between Israel and Egypt could flare up.

“There are certain discrete things the U.S. can do, like help manage the situation in Sinai,” he said, noting the increase in tensions after attempted terrorist attacks from the Egyptian peninsula bordering Israel. “That’s the flashpoint where political leaders have to do things are rational from their perspective, but that could lead to" an outbreak of conflict.

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